1. New Modes of Scholarly Communication and Learning Philip E. Bourne University of California San Diego pbourne@ucsd.edu 1WSU December 2, 2008

2. Disclaimer I am not an expert, but through my involvement with Open Access (OA) I have seen the possibilities for improved scholarly communication and learning It is this vision I would like to share with you today WSU December 2, 20082

3. Let me cast that vision into a scenario that we can dissect and study 3WSU December 2, 2008

4. The Vision… Prior to leaving home a UCSD graduate student syncs her IPOL with the latest papers delivered overnight by the journal via RSS feed. On the bus she reviews the stream, selecting a paper close to her interest in HIV-1 proteases. The data shows apparent anomalies with her own work. Being on-line she notices that a colleague has also discovered the same paper and they IM annotating the results. By the time the bus stops she has recomputed the results, proven the anomaly and made a rebuttal in the form of a “pubcast” to the Editor and sent it to the journal. 4WSU December 2, 2008

5. Science Fiction – Yes or No? I would argue that the only part of this vision that is science fiction is finding a bus in San Diego 5WSU December 2, 2008

6. Science Fiction? Five years ago Yes… Today No… Five years ago the idea of downloading data on a bus would have been absurd – not today Five years ago an IPOL would be absurd - not today (consider the smart phone) Journals and databases are providing RSS feeds today IM is prevalent but not for scientific discourse Video and podcasting are prevalent but not for scientific discourse Full text journal articles and data are on-line but not integrated 6WSU December 2, 2008

7. What is Missing to Make the Vision a Reality? 1.Seamless integration between the data and the publication upon which that data are based 2.Seamless integration of the authoring and publishing process 3.Notion of traditional publications being associated with podcasts and video 4.Professional networking akin to social networking 7WSU December 2, 2008

8. What are the Catalysts for Change? New publishing paradigms, most importantly open access publishing The emerging generation of digital scientists The increased ease of working with digital media, notably sound and video 8WSU December 2, 2008

9. SSPPS 2059 NIH Public Access Policy “The research supported by the National Institutes of Health (NIH) is essential to improving human health. Public access to this research is vital – today and for generations to come.” From a letter from NIH Director Zerhouni to grantees, February 3rd, 2005

10. SSPPS 20510 More and more authors care about improving access to their papers… “Faced with the option of submitting to an open-access or closed-access journal, we now wonder whether it is ethical for us to opt for closed access on the grounds of impact factor or preferred specialist audience.” -- Costello and Osrin in The Lancet

11. SSPPS 20511 Where are we Today? NIH and other government funders have mandated open access Full text increasingly on-line and potentially usable Traditional publishers have used the internet as a distribution medium, but the power of the medium has yet to be realized Data increasingly on-line but not integrated with the publication derived from it

12. The Growth of Open Access Literature 12WSU December 2, 2008

13. Open Access (Creative Commons License) 1.All published materials available on-line free to all (author pays model) 2.Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s) 3.Copyright remains with the author 13WSU December 2, 2008

14. Open Access (Creative Commons License) 1.All published materials available on-line free to all (author pays model) 2.Unrestricted access to all published material in various formats eg XML provided attribution is given to the original author(s) 3.Copyright remains with the author The catalyst PLoS Comp Biol 2008 4(3) e1000037 14WSU December 2, 2008

15. Community Reaction? Most scientists have no idea that this implies that anyone can take their material and enhance it e.g., via mashup and effectively republish it 15WSU December 2, 2008

16. Okay so much for the 1% inspiration, where is the 99% perspiration? 16WSU December 2, 2008

17. What is Missing to Make the Vision a Reality? 1.Seamless integration between the data and the publication upon which that data are based 2.Seamless integration of the authoring and publishing process 3.Notion of traditional publications being associated with podcasts and video 4.Professional networking akin to social networking PLoS Comp. Biol. 2005 1(3), e34 17WSU December 2, 2008

18. Database and Journal Integration- The Test Bed http://www.wwpdb.org/ Journals Database 18WSU December 2, 2008

19. The Protein Data Bank Paper not published unless data are deposited – strong data to literature correspondence Highly structured data conforming to an extensive ontology DOI’s assigned to every structure – http://www.doi.org http://www.pdb.org 19WSU December 2, 2008

20. Seamless Integration between Data and the Literature – What Does That Imply? Improving semantic consistency in the literature – best done at the point of authoring Post processing to establish semantic content New forms of visualization and interaction at the presentation layer 20WSU December 2, 2008

21. Seamless Integration between Data and the Literature – What Does That Imply? Improving semantic consistency in the literature – best done at the point of authoring Post processing to establish semantic content New forms of visualization and interaction at the presentation layer 21WSU December 2, 2008

22. 1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results BioLit: Tools for New Modes of Scientific Dissemination Biolit integrates biological literature and biological databases and includes: –A database of journal text –Authoring tools to facilitate database storage of journal text –Tools to make static tables and figures interactive 4. The composite view has links to pertinent blocks of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle http://biolit.ucsd.edu 22

23. http://biolit.ucsd.edu PSP Washington DC Feb. 2008 23

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27. ICTP Trieste, December 10, 2007 27WSU December 2, 2008

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29. What is Missing to Make the Vision a Reality? 1.Seamless integration between the data and the publication upon which that data are based 2.Seamless integration of the authoring and publishing process 3.Notion of traditional publications being associated with podcasts and video 4.Professional networking akin to social networking 29WSU December 2, 2008

30. Author Paper Word File in Docx format Publisher BioLit Plugin Project 30WSU December 2, 2008

31. Sidebar: Imagine a Future Where… The relationship between author and publisher is quite different The publisher is a warehouse for the workflow of scientific endeavor not just a repository for the end product Evidence: –www.researchgate.netwww.researchgate.net –MetaLab (Borya Shakhnovich) 31WSU December 2, 2008

32. BioLit Plugin Project Leverages Office Open XML used in Microsoft Office 2007 Custom schema attached to document and used to automatically XML tag ontology terms and database identifiers within a research paper Ontology tagging assists publication of scientific research by aiding efficient and accurate automated categorization and promotion of information dissemination Conversion of manuscript to NLM DTD for direct submission to publisher Automated Ontology & ID Tagging within Microsoft Word Documents 32WSU December 2, 2008

33. BioLit Plugin Project Rather than Post-processing the Document the Author Controls the Semantic Tagging 33WSU December 2, 2008

34. Plugin Architecture 34WSU December 2, 2008

35. Context-Sensitive Data Access Display of information of database entries when the user clicks on the ID in the document Display of ontology terms related to terms in the document text, using local database search 35WSU December 2, 2008

36. Ontologies are Stored in a Local Database 36WSU December 2, 2008

37. User Configurable Selection Fully user configuration ontology and database identifier selection All searches occur within the user’s desktop computer Desired ontologies are downloaded and installed automatically, and update periodically BioLit installer XML file provides the application with the information needed to download and install ontologies. 37WSU December 2, 2008

38. What is Missing to Make the Vision a Reality? 1.Seamless integration between the data and the publication upon which that data are based 2.Seamless integration of the authoring and publishing process 3.Notion of traditional publications being associated with podcasts and video 4.Professional networking akin to social networking PSP Washington DC Feb. 2008 38WSU December 2, 2008

39. YouTube for Scientists www.scivee.tv 39WSU December 2, 2008

40. Motivation 40WSU December 2, 2008

41. Pubcast – Video Integrated with the Full Text of the Paper 41

42. Pubcast - Making 42 WSU December 2, 2008

43. Channels – Just Like TV ICTP Trieste, December 2007 43

44. Professional Profile ICTP Trieste, December 2007 44

45. Create & Join Communities and Discussion Groups ICTP Trieste, December 2007 45

46. The Role of Ontologies Tag clouds generated automatically from MESH headings Semantic enrichment can be included with a pubcast 46WSU December 2, 2008

47. SciVee – Viral Projects Sweetwater School District “Postercasts” Science video competitions “CVcasts” 47WSU December 2, 2008

48. Acknowledgements SciVee Team –Apryl Bailey –Tim Beck –Leo Chalupa –Marc Friedman –Alex Ramos –Willy Suwanto BioLit Team J. Lynn Fink Sergey Kushch Marco Martinez Greg Quinn Parker Williams CT Watch 2007, 3(3) 26-31 48WSU December 2, 2008

49. Questions? pbourne@ucsd.edu 49WSU December 2, 2008